Chapters 8 (Final check at 9:00 AM 12/11/10. Looks basically complete)
8.1- An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics
Bioenergetics- study of how organisms manage their energy resources
- There are usable & unusable forms of energy
o Unusable= released as heat
o When things change form they loose energy
- Closed system= doesn’t exchange energy w/ surrounding environment (CAN reach equilibrium)
- Open system= energy is exchanged b/t system and surrounding environment (DOESN’T reach equilibrium)à humans
Metabolism- the totality of an organism’s chemical reactions (sum of all chemical reactions in a cell)à an emergent property of life—as it goes up levels more properties arise from the interactions b/t molecules within the cell.
Pathways- a series reaction where the product of one reaction is the reactant of the next—each one requires enzymes to catalyze reactions
- 2 types of metabolic pathways:
o Anabolic (anabolism)= reactions that need/ consume energy to build more complex molecules—“uphill”
§ Endergonic= consume energy (goes from less complicated to more complicated)
§ Ex: photosynthesis
o Catabolic (catabolism)= reactions that release energy by breaking down complex molecules into simpler compounds
§ Exergonic= release energy (goes from more complicated to less complicated)
§ Spontaneous= when action occurs and doesn’t need extra energy—will cause entropy somewhere else (has to get energy)
§ Ex: cellular respiration
Energy- the capacity to cause change
§ Kinetic= energy associated with motion
o Ex: heat (thermal energy)—random movement of molecules or atoms
§ Potential= energy that matter posses because of it’s location/ structure (stored energy)
o Ex: chemical energy—potential energy available for release in a chemical reaction (energy of covalent bondsà when food is broken down)
o Ex: water behind a dam/ mole of glucose
First Law of Thermodynamics (energy transformations) - Law of Conservation of Energy: energy can neither be created nor destroyed only changed from one form to another

Second Law of Thermodynamics- natural tendency is towards disorder/ randomness (entropy)
§ Energy is needed to keep things organized/maintain order in a system

8.2- The free-energy change of a reaction tells us whether the reaction occurs spontaneously.
· Free energy- the portion of a system’s energy available to perform work when temperature and pressure are uniform. ( ÙG or delta G. This was the closest I could get to a triangle on word).
· For an exergonic (spontaneous) reaction, ÙG is negative.
o Exergonic- net release of free energy
· For an endergonic reaction, ÙG is positive.
o Endergonic- must take energy from the surroundings
· Cellular respiration is an example of an exergonic reaction. (ÙG= -686 kcal/mol)
· The change in free energy during a reaction: ÙG= ÙH-TÙS, where ÙH is enthalpy (total energy of a system), ÙS is entropy (measure of disorder), and T is the temperature in Kelvin. In order for a reaction to be spontaneous (ÙG is negative), either H must decrease and/or S must increase.
· When ÙG is negative, there is less free energy after the reaction, causing the products to be more stable. More free energy= more change.
· The energy released by a exergonic reaction is equal to the energy required for the reverse endergonic reaction.

Section 8.3
3 Main kinds of work
· Mechanical : work of motion
· Transport: work of moving molecules
· Chemical: chemical reactions
Energy coupling: pairing a reaction that releases energy (exergonic) with one that needs energy (endergonic)
ATP: the cell’s energy shuttle, energy transport molecule
· 3 phosphate groups
· Ribose
· Adenine
Picture - pg 148 from our book (Fig. 8.8)
· ATP is an exergonic reaction (releases energy, spontaneous)
· When a bond between the phosphate group is broken by hydrolysis (adding of water) energy is released
· The energy that is released from ATP when the terminal phosphate bond is broken
· The release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves
· The energy from ATP that is released can help other reactions (from cellular functions)
· The amount of energy that is released from ATP is -7.3 kcal / mol
· All types of work are powered by ATP
· ATP is renewable (constantly putting the phosphate group on and off)
· ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecules
· The recipient molecule is now phosphorylated

· All three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP

· The Regeneration of ATP

o ATP is a renewable resource that is regenerated by addition of a phosphate group to ADP
o The energy to phosphorylate ADP comes from catabolic reactions in the cell
o The chemical potential energy temporarily stored in ATP drives most cellular work

Section 5.4
Catalysts:
· Speed up reactions
· Are not consumed or used up in the reaction
· Are used in small quantities b/c they are not consumed and can be used again
· Lower the activation energy of the reaction
Activation Energy:
· The initial investment of energy for starting a reaction
· The energy required to change the reactant molecules so than the bonds can changes
· An enzyme lowers the activation energy; ΔG is not affected by an enzyme
Enzymes:
· Catalytic Protein
· The reactant an enzyme works on: Substrate
· Where the reaction takes place: Active site
· Four mechanisms enzymes use to lower the activation energy:
1. The active site provides a template for two or more substrates to come together so the reaction can occur between them
2. The enzyme can stretch the substrate molecules towards their transition state
3. The active site is a microenvironment to help with the reaction
4. Direct participation of active site in the reaction
· Temperature, pH and the initial concentration of the substrate affects the rate of enzyme reaction
· Acid can denature proteins
Induced Fit:
· The shape of enzyme fits substrate (moves slightly)
· Brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction
Cofactors: small molecules that bind permanently or reversibly with enzymes necessary for catalytic function, coenzymes which are organic molecules ex: vitamins
Competitive inhibitors: compete with substrate for active site, this can be overcome by increasing the concentration of the substrates
Noncompetitive inhibitors: bind to a part of the enzyme separate from the active site and change the enzyme shape, prohibiting enzyme action

Section 8.5 Regulation of enzyme activity helps control metabolism
· Allosteric regulation- molecules inhibit or activate enzyme activity when they bond to a site other than the active site.
o It is similar to non-competitive inhibition, but allosteric regulation is not permanent and controlled by the cell
· Two types of allosteric regulation: allosteric activator and allosteric inhibitor
o An activator stabilizes the enzyme in the active position, in a sense holding the enzyme open so it can work.
o An inhibitor stabilizes the enzyme in its inactive form, stopping the reaction
Cooperativity: a form of allosteric regulation that can amplify enzyme activity
· IIn cooperativity binding by a substrate to one active site stablilizes favorable conformational changes at all other subunits
· This actually binds to the active site compared to the activator
Feedback inhibition: the end product of a metabolic pathway shuts down the pathway
· Feedback inhibition prevent a cell from wasting chemical resources by synthesizing more product than is needed
· Negative feedback

Chapter 41
Herbivores: animals that eat plants
Carnivores: animals that eat meat
Omnivores: animals that eat both plants and meat (humans)

Why we need to eat:
-fuel (energy)
-organic materials
-essential nutrients
Energy
-undernourished: not enough calories in a diet
-over nourished: too many calories in a diet, obesity
-malnourished: not enough essential nutrients in a diet (biggest global issue)
Organic Materials
-organic, raw materials used for biosynthesis
Essential Nutrients
-essential nutrients must be taken in by the body because they can’t be made
-four classes of essential nutrients: essential amino acids, essential fatty acids, vitamins, and minerals.

Essential amino acids: Animals require 20 amino acids to make proteins, and most animal species can synthesize about half of these, as long as their diet includes organic nitrogen. The remaining ones, the essential amino acids, must be obtained from food in prefabricated form. Eight amino acids are essential in the adult human diet; the same amino acids are essential for most animals. Amino acids can be found in meat, eggs, cheese, and other animal products.

Essential Fatty Acids: Animals can synthesize most of the fatty acids they need. The essential fatty acids, the ones they cannot make, are certain unsaturated fatty acids. The diets of humans and other animals generally furnish ample quantities of essential fatty acids, and thus deficiencies are rare.

Vitamins: Vitamins are organic molecules required in the diet in amounts that are quite small compared with the relatively large required quantities of essential amino acids and fatty acids. So far, 13 vitamins essential to humans have been identified. They have extremely diverse physiological functions. Vitamins are grouped into two categories: water–soluble vitamins and fat–soluble vitamins (D, E, A, K). Excesses of water–soluble vitamins are excreted in urine, and moderate overdoses of these vitamins are probably harmless. Fat-soluble vitamins are more likely because they are unable to flush out.

Minerals: Minerals are simple, inorganic nutrients. Mineral requirements vary in different animal species.

*Information comes from book website



Chapter 41: For Wikispaces
Adapted From Online Ap Biology Textbook Website
Campbell Biology 7th Edition
Chapter 41 Sections 41.4 and 41.5


Section 41.3

From the Student Study Guide for Biology:

The min stages of food processing are ingestion, digestion, absorption and elimination.
Ingestion is the act of eating. Digestion splits macromolecules into monomers by enzymatic hydrolysis, the addition of a water molecule when the bond between monomers is broken. Absorption is the when monomers and small molecules are absorbed into the cells of the animal. Elimination is when the undigested remainder of the food passes out through the digestive compartment.


Figure 41.15

From Online book:
Intracellular digestion is when food vacuoles with hydrolytic enzymes break down food without digesting the cell’s own cytoplasm. Digestion within a cell.
Extracellular digestion is when food is broken down outside of the cells.

From Student Study Guide:
A single-opening gastrovascular cavity functions in both digestion and transport of nutrients throughout the body. Gastrodermal cells take in food particles by phagocytosis and hydrolysis of macromolecules occurs within food vacules.

Most animals have complete digestive tracts or alimentary canals, with two openings, a mouth and an anus. Because food moves along the canal in a single direction, the tube can be organized into specialized regions that carry out digestion and nutrient absorption in a stepwise fashion


41.4 Part a.
-The mammalian digestive system consists of the alimentary canal and various accessory glands that secrete digestive juices into the canal through ducts
-.Peristalsis, rhythmic waves of contraction by smooth muscles in the wall of the canal, pushes the food along the tract.
-At some of the junctions between specialized segments of the digestive tube, the muscular layer is modified into ring-like valves called sphincters, which close off the tube like drawstrings, regulating the passage of material between chambers of the canal.
-The accessory glands of the mammalian digestive system are three pairs of salivary glands, the pancreas, the liver, and the gallbladder, which stores a digestive juice.
-Both physical and chemical digestion of food begin in the mouth. During chewing, teeth of various shapes cut, smash, and grind food, making it easier to swallow and increasing its surface area.
-he presence of food in the oral cavity triggers a nervous reflex that causes the salivary glands to deliver saliva through ducts to the oral cavity.
-Chemical digestion of carbohydrates, a main source of chemical energy, begins in the oral cavity. Saliva contains salivary amylase, an enzyme that hydrolyzes starch (a glucose polymer from plants) and glycogen (a glucose polymer from animals). The main products of this enzyme′s action are smaller polysaccharides and the disaccharide maltose.
-The tongue tastes food, manipulates it during chewing, and helps shape the food into a ball called a bolus. During swallowing, the tongue pushes a bolus to the back of the oral cavity and into the pharynx: The region we call our throat is the pharynx, a junction that opens to both the esophagus and the windpipe (trachea).
-When we swallow, the top of the windpipe moves up so that its opening, the glottis, is blocked by a cartilaginous flap, the epiglottis.
-The esophagus conducts food from the pharynx down to the stomach by peristalsis: wave like muscle movement
-The stomach stores food and performs preliminary steps of digestion. This large organ is located in the upper abdominal cavity, just below the diaphragm.
-Besides storing food, the stomach performs important digestive functions: It secretes a digestive fluid called gastric juice and mixes this secretion with the food by the churning action of the smooth muscles in the stomach wall.
-With a high concentration of hydrochloric acid, gastric juice has a pH of about 2 in the stomach
-Also present in gastric juice is pepsin, an enzyme that begins the hydrolysis of proteins.
-Pepsin is one of the few enzymes that works best in a strongly acidic environment. The low pH of gastric juice denatures (unfolds) the proteins in food, increasing exposure of their peptide bonds to pepsin.
-One of the stomach′s defenses against self–digestion is a coating of mucus, secreted by the epithelial cells of the stomach lining.
-As a result of mixing and enzyme action, what begins in the stomach as a recently swallowed meal becomes a nutrient–rich broth known as acid chyme.
-The opening from the esophagus to the stomach, the cardiac orifice, normally dilates only when a bolus arrives. The occasional back flow of acid chyme from the stomach into the lower end of the esophagus causes heartburn.


41.4
The small intestine:
Most enzymatic hydrolysis of macromolecules and nutrient absorption into the blood takes places in the
small intestine
Digestive juices (from the pancreas, liver, gallbladder, and gland cells of the intestinal wall) are mixed with the chyme in the duodenum, the first section of the small intestine.
The Liver produces bile which is stored in the gallbladder until needed. It aids in the digestion of fats and contains pigments that are by-products of the breakdown of red blood cells in the liver.
Circular folds of the small intestine lining are covered with fingerlike projections called villi, that on which the epithelial cells have microscopic extensions called microvilli, creating a huge surface area for absorption.
Penetrating the core of each villus is a net of microscopic blood vessels (capillaries) and a small vessel of the lymphatic system called a lacteal.
In contrast to the lacteals, the capillaries and veins that drain nutrients away from the villi all converge into the liver.

Figure 41.19

41.5:

-Dentition, an animal′s assortment of teeth, is one example of structural variation reflecting diet
-Large, expandable stomachs are common in carnivores, which may go for a long time between meals and therefore must eat as much as they can when they do catch prey.
-The length of the vertebrate digestive system is also correlated with diet. In general, herbivores and omnivores have longer alimentary canals relative to their body size than carnivores.
-Vegetation is more difficult to digest than meat because it contains cell walls. A longer tract furnishes more time for digestion and more surface area for the absorption of nutrients.
-Herbivorous animals face a nutritional challenge: Much of the chemical energy in their diets is contained in the cellulose of plant cell walls, but animals do not produce enzymes that hydrolyze cellulose.
-Many vertebrates (as well as termites, whose wood diets are largely cellulose) solve this problem by housing large populations of symbiotic bacteria and protists in fermentation chambers in their alimentary canals.
-Our bodies provide a warm place for the bacteria to live, and the bacteria make our bodies vitamins and sometime hydrogen sulfide gas.
-Many herbivorous mammals, including horses, house symbiotic microorganisms in a large cecum, the pouch where the small and large intestines connect.
-The most elaborate adaptations for an herbivorous diet have evolved in the animals called ruminants**, which include deer, cattle, and sheep